MUSC scientists identify first Omicron cases in South Carolina

December 15, 2021
Graphic image of Omicron variant
The Omicron variant was first reported to the World Health Organization less than a month ago. It has since spread to countries around the world. iStock

Scientists at the Medical University of South Carolina have identified the first cases of the Omicron variant in the state. Julie Hirschhorn, Ph.D., directs the molecular pathology lab that found them. “It is three cases, all of them in the Lowcountry. Two out of the three were fully vaccinated, but not boosted. And one had only one dose of the vaccine.”

One is in Charleston, another in North Charleston and the third on Johns Island. 

Hirschhorn’s lab sequences all COVID cases that come through MUSC for testing. Sequencing involves looking at the virus’s genome to check for variants. The scientists sequence in batches they call runs.

“Since the identification of Omicron in Africa, we've been trying to do a run each week to make sure that we're sequencing as real time as possible. The more real time you do sequencing, the better handle you have on what's going on in the population,” she said.

The first Omicron case in South Carolina involved a COVID sample collected for testing on Dec. 4. That means the fast-spreading variant has been here for at least a couple of weeks.

Dr. Julie Hirschhorn talks with Kristen Maurer, a medical technologist who is indexing each coronavirus-positive sample so 384 samples can be sequenced at the same time. 
Dr. Julie Hirschhorn, left, works with medical technologist Kristen Maurer to prepare samples for sequencing. Photo by Sarah Pack

Based on Omicron’s track record elsewhere, the numbers could rise quickly. “When a new variant is identified, the first thing that we can really get a good handle on is transmission, because we watch the number of cases and how quickly that increases. And Omicron is pretty prevalent right now over in the U.K. The U.K. seems to be doubling Omicron cases about every day,” Hirschhorn said.

“So it does seem to be more transmissible than Delta. There's not a whole lot of evidence about severity of disease yet, because we're just starting to see the hospitalizations. In Australia, hospitalizations are pretty low. The hospitalizations in the U.K. also appear to, in early terms, suggest that it's maybe more mild disease. That’s great, except that if you have COVID circulating in large quantities, then you always have that ability for more mutations to happen. And so I think it's pretty critical that people try and protect themselves in any way that they can.”

She encouraged people to get booster shots. “All three of our Omicron cases were in people at least six months out from their latest shot. The data supports that if you're six months out, you should probably get boosted,” Hirschhorn said.

Her team will continue to look for Omicron and keep the public informed about its findings. “Now, for our lab, the most important thing is to continue sequencing to look at our transmission rate in South Carolina. We've been very fortunate with the CARES Act dollars and the support from the state to do consistent testing across the state and surveillance,” she said.

“And so, because the state has supported us, we really feel the need to support the state back. Being one of the leading medical centers in South Carolina, it's very important to us that we inform our population; that we stay on top of their health and any issues that might arise. And so I plan on continuing to sequence as much, and as often as we can, because I do feel like this knowledge really empowers people to make decisions that will impact them.”

The molecular pathology team at MUSC has played a leading role in providing that kind of knowledge since the early days of the pandemic. When the coronavirus arrived, the lab quickly ramped up for COVID testing, working with sites across the state. It began sequencing for variants last spring and sharing its findings with the public. Along the way, it identified mutations of the Delta variant, including one so prevalent that it may get its own name.

Now, as we head into the winter holidays, COVID cases are on the rise in South Carolina. Most involve the Delta variant. While knowing which variants are circulating is important because it tells us how the virus is changing and spreading, Hirschhorn said it’s less valuable for individuals to know which variant they were infected with because it won’t change the treatment they get. COVID is COVID. And it’s still here as we head into another holiday season.

“I encourage people to consider risk stratification going into the holiday season and just being cognizant of what you want to do and finding a way to do it that's safer,” Hirschhorn said.